dorado: "-o" is now ambiguous: refers to both output directory and "overlap"

[GabeAl]

Issue Report

Please describe the issue:

dorado 0.8.2.

Output arguments (detailed usage):
  --min-qscore                Discard reads with mean Q-score below this threshold. [nargs=0..1] [default: 0]
  --emit-moves                Write the move table to the 'mv' tag.
  --emit-fastq                Output in fastq format.
  --emit-sam                  Output in SAM format.
  -o, --output-dir            Optional output folder, if specified output will be written to a calls file (calls_<timestamp>.sam|.bam|.fastq) in the given folder.

See "o" above.

Now consider:

Advanced arguments (detailed usage):
  -b, --batchsize             The number of chunks in a batch. If 0 an optimal batchsize will be selected. [nargs=0..1] [default: 0]
  -c, --chunksize             The number of samples in a chunk. [nargs=0..1] [default: 10000]
  -o, --overlap               The number of samples overlapping neighbouring chunks. [nargs=0..1] [default: 500]

Trying to specify output directory using shorthand leads to the error: [2024-10-23 20:38:09.539] [error] Failed to parse 'output_dir' as decimal integer: pattern 'output_dir' not found

Steps to reproduce the issue:

Run the software with the -o flag to specify output directory. It will treat it as "--overlap" instead of "--output-dir"

[malton-ont]

Hi @GabeAl,

Thanks for reporting this. This is already covered by https://github.com/nanoporetech/dorado/issues/1037 - please follow that issue for updates.